The B-phycoerythrin hexamer (αβ)6γ of Porphyridium purpureum was isolated and purified. The absorption, circular dichroism, fluorescence and ultrafast time-resolved spectra were obtained. The results showed a double absorption peak at 545 nm and 565 nm and a shoulder peak at 498 nm, and fluorescence emission maxima at 580 nm and 620 nm were observed. The circular dichroism spectra in the near-ultraviolet region were obtained and resolved for the first time, which showed that the two peaks at 260 nm and 305 nm were considered to be correlated to phenylalanine (Phe) and tryptophan (Trp) in a conservative hydrophobic microenvironment, respectively. The circular dichroism spectra in the visible region showed that PEB139α/PEB158β and PEB82α/PEB82β existed as two exciton-coupled bilin pairs. Energy transfer within the exciton-coupled pairs was by exciton splitting, while between the exciton-coupled pairs was by Förster resonance. From the studies of the energy transfer dynamics by ultrafast time-resolved fluorescence spectroscopy, it was confirmed that the energy transfer of the B-PE hexamer had three time components of 8 ps, 60 ps, and 1200 ps. In addition, the internal energy transfer pathways of B-phycoerythrin hexamer were identified by deconvoluting the fluorescence decay curve at different detection wavelengths.